EvidentialGene source code changes, 2019may to 2020jan .. to 2020mar04

Major new script versions are 
  tr2aacds4.pl and evgpipe_sra2genes4v.pl
    with updates and additions of associated pipeline components.
  tr2ncrna.pl  : new pipeline to select non-coding RNA subset of input transcripts

Major component revisions
  cdna_bestorf.pl, cdna_proteins.pm : revised bestorf calculations following tests
  blasttrset2exons2.pl : new measurement script, exon chain analysis for alternate transcripts
  trclass_resolve_strandmix.pl : resolve genes w/ mixed-strand CDS alternates
  asmrna_dupfilter4.pl  : classify transcripts by self-alignment, with new,updated measures
  asmrna_altreclass4.pl : reclassify alternates and noclass using new,updated measures
  trclass2pubset.pl : revised sequence set publication
  
Useful additions
  altparclassify.pl : classify transcript set as to alternate/paralog by self-alignment
  cdshexprob.pl     : calculate CDS coding potential from transcript CDS - UTR hexamers
  cdsalignkaks.pl   : calculate KaKs statistics for CDS-alignments, 
                       of two species/pops with KaKs_Calculator and blastn
  evg_buscogenesum.pl,evg_busco2v.py, : measure BUSCO conserved genes, for Evg gene IDs

evigene19may_20jan30.diff - only.evigene19may14
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Update  evigene20jan30/scripts/altbest.pl
Update  evigene20jan30/scripts/cdna_bestorf.pl
Update  evigene20jan30/scripts/cdna_evigenesub.pm
Update  evigene20jan30/scripts/cdna_proteins.pm
Update  evigene20jan30/scripts/evgpipe_sra2genes.pl : use evgpipe_sra2genes4v.pl
New     evigene20jan30/scripts: evgpipe_sra2genes4v.pl  : production
Update  evigene20jan30/scripts/evigene_pubsets.pm
New     evigene20jan30/scripts/genes: altparclassify.pl : production, maybe
Update  evigene20jan30/scripts/genes/blast2evgff.pl
New     evigene20jan30/scripts/genes: blasttrset2exons2.pl : production
New     evigene20jan30/scripts/genes: commonexons.pl  : test
Update  evigene20jan30/scripts/genes/evg17_scripts/corntrsetbltab.pl
Update  evigene20jan30/scripts/genes/evg17_scripts/run_cdsaln_kaks.sh
Update  evigene20jan30/scripts/genes/evgpubsetsum.pm
New     evigene20jan30/scripts/genes: run_s07p_tr2cdspub.sh : dev,test
Update  evigene20jan30/scripts/genes/trclass2pubset.pl
New     evigene20jan30/scripts/genes: trclass_resolve_strandmix.pl : production
Update  evigene20jan30/scripts/makeblastscore.pl  : -> makeblastscore3
Update  evigene20jan30/scripts/makeblastscore3.pl
New     evigene20jan30/scripts/prot: aanstat.pl
Update  evigene20jan30/scripts/prot/aaqual.sh
New     evigene20jan30/scripts/prot: cdsalignkaks.pl
New     evigene20jan30/scripts/prot: cdshexprob.pl  : production
Update  evigene20jan30/scripts/prot/cdsqual.pl
New     evigene20jan30/scripts/prot: cdsqual.sh
New     evigene20jan30/scripts/prot: make_consensus.pl  : dev,test
Update  evigene20jan30/scripts/prot/namegenes.pl
Update  evigene20jan30/scripts/prot/protein_names.pm
Update  evigene20jan30/scripts/prot/tr2aacds.pl   : -> tr2aacds4.pl
Update  evigene20jan30/scripts/prot/tr2aacds2.pl
New     evigene20jan30/scripts/prot: tr2aacds2d.pl  : dev
New     evigene20jan30/scripts/prot: tr2aacds3.pl : dev
New     evigene20jan30/scripts/prot: tr2aacds4.pl : production
New     evigene20jan30/scripts/prot: tr2aacds4a.pl  : test
Update  evigene20jan30/scripts/prot/traa2cds.pl
Update  evigene20jan30/scripts/prot/trclass2mainalt.pl
New     evigene20jan30/scripts/rnaseq: asmrna_altreclass3c.pl : production, becomes v4
New     evigene20jan30/scripts/rnaseq: asmrna_altreclass4.pl  : -> asmrna_altreclass3c.pl
Update  evigene20jan30/scripts/rnaseq/asmrna_dupfilter3c.pl
New     evigene20jan30/scripts/rnaseq: asmrna_dupfilter4.pl : -> asmrna_dupfilter4a.pl
New     evigene20jan30/scripts/rnaseq: asmrna_dupfilter4a.pl  : production, v4
New     evigene20jan30/scripts/rnaseq: asmrna_identityclass4a.pl  : dev
New     evigene20jan30/scripts/rnaseq: asmrna_overlocusclass4a.pl : dev
Update  evigene20jan30/scripts/rnaseq/fa2pairfa.pl
New     evigene20jan30/scripts: run_evgsra2genes4v.sh : example
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Documents
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evigene/docs/evg4docs/

https://sourceforge.net/p/evidentialgene/blog/2020/03/reference-protein-annotation-with-namegenes/
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